After reading this chapter, you should:

To load a package that is already installed on your machine, you call the library function. It is widely agreed that calling this function library was a mistake, and that calling it load_package would have saved a lot of confusion, but the function has existed long enough that it is too late to change it now. To clarify the terminology, a package is a collection of R functions and datasets, and a library is a folder on your machine that stores the files for a package.^[30]

If you have a standard version of R—that is, you haven’t built some custom version from the source code—the lattice package should be installed, but it won’t automatically be loaded. We can load it with the library function:

library(lattice)

We can now use all the functions provided by lattice. For example, Figure 10-1 displays a fancy dot plot of the famous Immer’s barley dataset:

dotplot(
  variety ~ yield | site,
  data   = barley,
  groups = year
)

Notice that the name of the package is passed to library without being enclosed in quotes. If you want to programmatically pass the name of the package to library, then you can set the argument character.only = TRUE. This is mildly useful if you have a lot of packages to load:

pkgs <- c("lattice", "utils", "rpart")
for(pkg in pkgs)
{
  library(pkg, character.only = TRUE)
}

Figure 10-1. A dot plot of Immer’s barley data using lattice

If you use library to try to load a package that isn’t installed, then it will throw an error. Sometimes you might want to handle the situation differently, in which case the require function provides an alternative. Like library, require loads a package, but rather than throwing an error it returns TRUE or FALSE, depending upon whether or not the package was successfully loaded:

if(!require(apackagethatmightnotbeinstalled))
{
  warning("The package 'apackagethatmightnotbeinstalled' is not available.")
  #perhaps try to download it
  #...
}

search()

## [1] ".GlobalEnv"        "package:stats"     "package:graphics"
## [4] "package:grDevices" "package:utils"     "package:datasets"
## [7] "package:methods"   "Autoloads"         "package:base"

View(installed.packages())

R.home("library")   #or

## [1] "C:/PROGRA~1/R/R-devel/library"

.Library

## [1] "C:/PROGRA~1/R/R-devel/library"

path.expand("~")    #or

## [1] "C:\Users\richie\Documents"

Sys.getenv("HOME")

## [1] "C:\Users\richie\Documents"

.libPaths()

## [1] "D:/R/library"
## [2] "C:/Program Files/R/R-devel/library"

Factory-fresh installs of R are set up to access the CRAN package repository (via a mirror—you’ll be prompted to pick the one nearest to you), and CRANextra if you are running Windows. CRANextra contains a handful of packages that need special attention to build under Windows, and cannot be hosted on the usual CRAN servers. To access additional repositories, type setRepositories() and select the repositories that you want. Figure 10-2 shows the available options.

Figure 10-2. List of available package repositories

Bioconductor contains packages related to genomics and molecular biology, while R-Forge and RForge.net mostly contain development versions of packages that eventually appear on CRAN. You can see information about all the packages that are available in the repositories that you have set using available.packages (be warned—there are thousands, so this takes several seconds to run):

View(available.packages())

As well as these repositories, there are many R packages in online repositories such as GitHub, Bitbucket, and Google Code. Retrieving packages from GitHub is particularly easy, as discussed below.

Many IDEs have a point-and-click method of installing packages. In R GUI, the Packages menu has the option “Install package(s)…” to install from a repository and “Install package(s) from local zip files…” to install packages that you downloaded earlier. Figure 10-3 shows the R GUI menu.

You can also install packages using the install.packages function. Calling it without any arguments gives you the same GUI interface as if you’d clicked the “Install package(s)…” menu option. Usually, you would want to specify the names of the packages that you want to download and the URL of the repository to retrieve them from. A list of URLs for CRAN mirrors is available on the main CRAN site.

Figure 10-3. Installing packages in R GUI

This command will (try to) download the time-series analysis packages xts and zoo and all the dependencies for each, and then install them into the default library location (the first value returned by .libPaths):

install.packages(
  c("xts", "zoo"),
  repos = "http://www.stats.bris.ac.uk/R/"
)

To install to a different location, you can pass the lib argument to install.packages:

install.packages(
  c("xts", "zoo"),
  lib   = "some/other/folder/to/install/to",
  repos = "http://www.stats.bris.ac.uk/R/"
)

Obviously, you need a working Internet connection for R to be able to download packages, and you need sufficient permissions to be able to write files to the library folder. Inside corporate networks, R’s access to the Internet may be restricted. Under Windows, you can get R to use internet2.dll to access the Internet, making it appear as though it is Internet Explorer and often bypassing restrictions. To achieve this, type:

setInternet2()

If all else fails, you can visit http://<cran mirror>web/packages/available_packages_by_name.html and manually download the packages that you want (remember to download all the dependencies too), then install the resultant tar.gz/tgz/zip file:

install.packages(
  "path/to/downloaded/file/xts_0.8-8.tar.gz",
  repos = NULL,       #NULL repo means "package already downloaded"
  type = "source"     #this means "build the package now"
)

install.packages(
  "path/to/downloaded/file/xts_0.8-8.zip",
  repos = NULL,       #still need this
  type = "win.binary" #Windows only!
)

To install a package directly from GitHub, you first need to install the devtools package:

install.packages("devtools")

The install_github function accepts the name of the GitHub repository that contains the package (usually the same as the name of the package itself) and the name of the user that maintains that repository. For example, to get the development version of the reporting package knitr, type:

library(devtools)
install_github("knitr", "yihui")

After your packages are installed, you will usually want to update them in order to keep up with the latest versions. This is done with update.packages. By default, this function will prompt you before updating each package. This can become unwieldy after a while (having several hundred packages installed is not uncommon), so setting ask = FALSE is recommended:

update.packages(ask = FALSE)

Very occasionally, you may want to delete a package. It is possible to do this by simply deleting the folder containing the package contents from your filesystem, or you can do it programmatically:

remove.packages("zoo")